.glm.linear
Linear regression from --glm (quantitative phenotype). Header line starts with '#'. Column set can be reduced with cols=; optional NEG_LOG10_P and joint F_STAT appear with modifiers.
Overview
| Field |
Value |
| Format key |
plink2_linear |
| Spec file |
formats/plink2_linear.json |
| Cite name |
PLINK 2.0 |
| Version |
PLINK 2.0 (doc revision 11 Mar 2026) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/2.0/formats#glm_linear |
| Citation |
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| NA value |
. |
| Comment prefix |
# |
| Header row |
yes |
| Column order |
#CHROM, POS, ID, REF, ALT1, ALT, PROVISIONAL_REF?, A1, OMITTED, A1_CT, ALLELE_CT, A1_FREQ, MACH_R2, TEST, OBS_CT, BETA, SE, L95, U95, T_STAT, F_STAT, P, ERRCODE, LOG10_P |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
#CHROM |
CHR |
— |
A1 |
EA |
— |
A1_CT |
— |
— |
A1_FREQ |
EAF |
— |
ALLELE_CT |
— |
— |
ALT |
ALT |
— |
ALT1 |
— |
— |
BETA |
BETA |
— |
CHROM |
CHR |
— |
ERRCODE |
— |
— |
F_STAT |
F |
— |
ID |
SNPID |
rsID |
L95 |
BETA_95L |
— |
LOG10_P |
MLOG10P |
— |
MACH_R2 |
INFO |
— |
OBS_CT |
N |
— |
OMITTED |
— |
— |
P |
P |
— |
POS |
POS |
— |
PROVISIONAL_REF? |
— |
— |
REF |
REF |
— |
SE |
SE |
— |
T_STAT |
T |
— |
TEST |
— |
— |
U95 |
BETA_95U |
— |
| ## Header descriptions |
|
|
| Column |
Description |
#CHROM |
Chromosome code |
A1 |
Counted allele in regression |
A1_CT |
Total A1 allele count |
A1_FREQ |
A1 allele frequency |
ALLELE_CT |
Allele observation count |
ALT |
All alternate alleles (comma-separated) |
ALT1 |
First alternate allele |
BETA |
Regression coefficient for A1 |
ERRCODE |
Reason for NA result |
F_STAT |
F-statistic (joint tests) |
ID |
Variant ID |
L95 |
Lower symmetric approx. CI for beta (--ci) |
LOG10_P |
Optional -log10(p) column |
MACH_R2 |
MaCH imputation R-squared |
OBS_CT |
Samples in regression |
OMITTED |
Omitted allele |
P |
Asymptotic p-value |
POS |
Base-pair coordinate |
PROVISIONAL_REF? |
Whether REF is provisional |
REF |
Reference allele |
SE |
Standard error of beta |
T_STAT |
t-statistic (linear model) |
TEST |
Test identifier |
U95 |
Upper symmetric approx. CI for beta (--ci) |
| ## Coverage |
|
8/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
partial |
EA |
NEA |
| Effect size |
yes |
BETA |
OR, HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P, MLOG10P |
— |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
|
|